A number of different poly- and oligo-nucleotides have been described for use in targeted alteration of nucleic acid sequence including chimeric RNA-DNA oligonucleotides that fold into a double-stranded, double hairpin conformation and single-stranded chemically modified oligonucleotides. These oligonucleotides have been shown to effect targeted alteration of single base pairs as well as frameshift alterations in a variety of host organisms, including bacteria, fungi, plants and animals.
Several cellular pathways and gene groups are believed to be involved in mediating in vivo repair of DNA lesions resulting from radiation or chemical mutagenesis, including the RAD52 epistasis group of proteins, the mismatch repair group of proteins and the nucleotide excision repair group of proteins. The role of these proteins in homologous recombination and maintaining genome integrity has been extensively studied and is reviewed, for example, in Heyer, Experientia 50(3), 223–233 (1994); Thacker, Trends in Genetics 15(5), 166–168 (1999); Paques & Haber, Microbiol. and Molec. Biol. Rev. 63(2), 349–404 (1999); and Thompson & Schild, Mutation Res. 477, 131–153 (2001). The specific function of these proteins in oligonucleotide-directed nucleic acid sequence alteration is not well understood.
The utility of oligonucleotide-directed nucleic acid sequence alteration as a means, for example, to generate agricultural products with enhanced traits or to generate animal models or animals with desired traits is affected by its frequency. The utility of oligonucleotide-directed nucleic acid sequence alteration as a therapeutic method would also be enhanced by increasing its efficiency. A need exists for methods to enhance the efficiency of oligonucleotide-directed nucleic acid sequence alteration.